|
| Status |
Public on Feb 18, 2021 |
| Title |
E12 |
| Sample type |
SRA |
| |
|
| Source name |
bacteria
|
| Organism |
Pseudomonas aeruginosa PAO1 |
| Characteristics |
genotype: delta-rhlE1
|
| Treatment protocol |
Cells were harvested using the RNA bacteria protect solution (QIAGEN).
|
| Growth protocol |
Swarming plates consisted of 0.5% (wt/vol) Difco bacto-agar with MMP medium supplemented with 20 mM glucose and 0.1% (w/v) casamino acids. Cells were inoculated onto swarm plates using 5µl of standardized overnight cultures and incubated overnight at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs was extracted and purified using Monarch RNA isolation kit (NEB), treated with DNase I (Promega) three times to remove contaminating genomic DNA and re-purified again using phenol-chloroform.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
replicate 2
Swarming cells
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Reads were trimmed using fastp 0.20.0, mapped using bowtie2 2.3.4.3.
Reads were counted using HTSeq 0.11.1.
Genome_build: NC_002516.2
Supplementary_files_format_and_content: tab-delimited text files include
|
| |
|
| Submission date |
Feb 17, 2021 |
| Last update date |
Feb 19, 2021 |
| Contact name |
Martina Valentini |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Geneva
|
| Department |
Department of Microbiology and Molecular Medicine
|
| Street address |
1, rue Michel Servet
|
| City |
Geneva |
| ZIP/Postal code |
1211 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL18782 |
| Series (1) |
| GSE166986 |
The DEAD-box RNA helicases RhlE2 is a global regulator of Pseudomonas aeruginosa lifestyle and pathogenesis |
|
| Relations |
| BioSample |
SAMN17970364 |
| SRA |
SRX10121833 |
